notebooks/DFT-dataset-generation.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "e4c8b28c",
   "metadata": {},
   "source": [
    "Copyright (c) 2023 Graphcore Ltd. All rights reserved.\n",
    "\n",
    "# DFT dataset generation using PySCF IPU\n",
    "\n",
    "This notebook shows how to generate DFT datasets on the Graphcore IPU based on\n",
    "\"PySCFIPU: Repurposing Density Functional Theory to Suit Deep Learning\", Mathiasen et al, (SynS & ML) Workshop, ICML 2023\n",
    "\n",
    "https://icml.cc/virtual/2023/28485\n",
    "\n",
    "Density Functional Theory (DFT) accurately predicts the properties of molecules given their atom types and positions,\n",
    "and often serves as ground truth for molecular property prediction tasks.\n",
    "Research in other areas of machine learning has shown that generalisation performance \n",
    "of Neural Networks tends to improve with increased dataset size, however, \n",
    "the computational cost of DFT has limited the size of DFT datasets.\n",
    "\n",
    "PySCF_IPU allowed us to create QM10X, a dataset with 100 million conformers, in 3000 IPU-hours.\n",
    "\n",
    "This notebook, running on 4 IPUs on Paperspace, creates 100K conformers in about 1 hour;\n",
    "it can be run on multiple 16-IPU systems (paid instances) to generate the full dataset."
   ]
  },
  {
   "cell_type": "markdown",
   "id": "e5faf299",
   "metadata": {},
   "source": [
    "Install `pyscf-ipu`:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "5f54d5a7",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2023-09-21T17:22:48.413594Z",
     "iopub.status.busy": "2023-09-21T17:22:48.413357Z",
     "iopub.status.idle": "2023-09-21T17:22:59.171899Z",
     "shell.execute_reply": "2023-09-21T17:22:59.171228Z",
     "shell.execute_reply.started": "2023-09-21T17:22:48.413568Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Obtaining file:///notebooks\n",
      "  Preparing metadata (setup.py) ... \u001b[?25ldone\n",
      "\u001b[?25hCollecting jax@ https://github.com/graphcore-research/jax-experimental/releases/download/jax-v0.3.16-ipu-beta3-sdk3/jax-0.3.16%2Bipu-py3-none-any.whl\n",
      "  Using cached https://github.com/graphcore-research/jax-experimental/releases/download/jax-v0.3.16-ipu-beta3-sdk3/jax-0.3.16%2Bipu-py3-none-any.whl (1.2 MB)\n",
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      "  Downloading https://github.com/graphcore-research/jax-experimental/releases/download/jax-v0.3.16-ipu-beta3-sdk3/jaxlib-0.3.15%2Bipu.sdk320-cp38-none-manylinux2014_x86_64.whl (111.3 MB)\n",
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      "\u001b[?25hCollecting tessellate-ipu@ git+https://github.com/graphcore-research/tessellate-ipu.git@main\n",
      "  Cloning https://github.com/graphcore-research/tessellate-ipu.git (to revision main) to /tmp/pip-install-mb470ioz/tessellate-ipu_258fa1046cdf4b848d1a67b623862219\n",
      "  Running command git clone --filter=blob:none --quiet https://github.com/graphcore-research/tessellate-ipu.git /tmp/pip-install-mb470ioz/tessellate-ipu_258fa1046cdf4b848d1a67b623862219\n",
      "  Resolved https://github.com/graphcore-research/tessellate-ipu.git to commit e254e597bc9b2ffdfa6e3f6d814bebde9bd2f716\n",
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      "Installing collected packages: pyscf-ipu\n",
      "  Attempting uninstall: pyscf-ipu\n",
      "    Found existing installation: pyscf-ipu 0.0.1\n",
      "    Can't uninstall 'pyscf-ipu'. No files were found to uninstall.\n",
      "  Running setup.py develop for pyscf-ipu\n",
      "Successfully installed pyscf-ipu\n",
      "\u001b[33mWARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead: https://pip.pypa.io/warnings/venv\u001b[0m\u001b[33m\n",
      "\u001b[0mNote: you may need to restart the kernel to use updated packages.\n",
      "install done\n"
     ]
    }
   ],
   "source": [
    "# PySCF IPU dependencies \n",
    "%pip install -e \"..[ipu]\"\n",
    "print('install done - restart kernel if packages where installed')"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "16f39a33",
   "metadata": {},
   "source": [
    "# Download and preprocess GDB 11 dataset"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "88c260e3",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2023-09-21T17:25:16.225823Z",
     "iopub.status.busy": "2023-09-21T17:25:16.225416Z",
     "iopub.status.idle": "2023-09-21T17:25:16.239357Z",
     "shell.execute_reply": "2023-09-21T17:25:16.238219Z",
     "shell.execute_reply.started": "2023-09-21T17:25:16.225799Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Found ./data/gdb11_size09_sorted.csv\n"
     ]
    }
   ],
   "source": [
    "import os\n",
    "from  gdb import sortgdb # Restart kernel if gdb not found - it was installed above\n",
    "\n",
    "gdb_filename = \"./data/gdb11_size09.smi\"\n",
    "out_filename = gdb_filename.replace(\".smi\", \"_sorted.csv\")\n",
    "\n",
    "loaded = os.path.exists(out_filename) and os.path.getsize(out_filename) == 6985727\n",
    "\n",
    "if loaded:\n",
    "  print(f'Found {out_filename}')\n",
    "else:\n",
    "  print(f'Did not find {out_filename}, or size was wrong')\n",
    "\n",
    "  # Download and extract GDB11 dataset.\n",
    "  !mkdir -p ./data\n",
    "  !wget -p -O ./data/gdb11.tgz https://zenodo.org/record/5172018/files/gdb11.tgz\\?download\\=1\n",
    "  !tar -xvf ./data/gdb11.tgz --directory ./data\n",
    "\n",
    "  # Filter & sort GDB11 dataset (size 9).\n",
    "  gdb_sorted = sortgdb.sort_gdb(gdb_filename, keep_only_atoms_count=9)\n",
    "  # Save output as csv.\n",
    "  gdb_sorted.to_csv(out_filename, index=False, header=False)\n",
    "  print('done')\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "a9da90c6",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2023-09-21T17:25:50.209218Z",
     "iopub.status.busy": "2023-09-21T17:25:50.208877Z",
     "iopub.status.idle": "2023-09-21T17:25:50.213530Z",
     "shell.execute_reply": "2023-09-21T17:25:50.212888Z",
     "shell.execute_reply.started": "2023-09-21T17:25:50.209196Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "import done\n"
     ]
    }
   ],
   "source": [
    "import os\n",
    "\n",
    "# PySCF IPU setup: use a single device per process.\n",
    "os.environ[\"JAX_IPU_DEVICE_COUNT\"] = \"1\"\n",
    "# JAX/XLA IPU compilation cache.\n",
    "os.environ['TF_POPLAR_FLAGS'] = \"\"\"\n",
    "  --executable_cache_path=/tmp/ipu-ef-cache\n",
    "\"\"\"\n",
    "\n",
    "# First import of JAX and TessellateIPU may take a few minutes...\n",
    "import jax\n",
    "import tessellate_ipu\n",
    "print('import done')"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "fa46c38d",
   "metadata": {},
   "source": [
    "# Create a DFT dataset using PySCF IPU\n",
    "\n",
    "In the following example, we use only a single IPU. Multiple IPUs can be used by simply launching a collection of PySCF IPU processes instead of a single one."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "96ea8a6f",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2023-09-21T17:26:20.435072Z",
     "iopub.status.busy": "2023-09-21T17:26:20.434581Z",
     "iopub.status.idle": "2023-09-21T17:26:20.469210Z",
     "shell.execute_reply": "2023-09-21T17:26:20.468642Z",
     "shell.execute_reply.started": "2023-09-21T17:26:20.435051Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[BASIS] STO-3G\n",
      "Loaded 444285 molecules from gdb11_size09\n"
     ]
    }
   ],
   "source": [
    "# Equivalent to command line:\n",
    "# python pyscf_ipu/dft.py  -generate  -save  -fname \"notebook_dataset\"\n",
    "#        -level 0  -plevel 0  -num_conformers 1000\n",
    "#        -gdb 9  -float32\n",
    "\n",
    "import time\n",
    "from pyscf_ipu.dft import get_args, process_args\n",
    "\n",
    "args = get_args([])\n",
    "args.backend = 'cpu'\n",
    "args.generate = True\n",
    "args.save = True\n",
    "args.fname = \"notebook_dataset\"\n",
    "\n",
    "args.level = 0\n",
    "args.plevel = 0\n",
    "\n",
    "args.float32 = True\n",
    "\n",
    "quick = True # Set to False to generate full dataset (takes some time)\n",
    "\n",
    "if quick:\n",
    "  args.id = 1\n",
    "  args.num_conformers = 32 # Set to 1000 for full dataset\n",
    "  args.limit = 33 # Comment out for full dataset\n",
    "else:\n",
    "  args.num_conformers = 1000\n",
    "\n",
    "process_args(args)\n",
    "\n",
    "# Load GDB09 data\n",
    "args.gdb = 1 # positive => split for multi ipus\n",
    "args.split = [0,1] # Partition 0 of 1 (i.e. single IPU)\n",
    "gdb = 'gdb11_size09'\n",
    "args.smiles = open(f\"data/{gdb}_sorted.csv\", \"r\").read().split(\"\\n\")\n",
    "print(f'Loaded {len(args.smiles)} molecules from {gdb}')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "41564018",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2023-09-21T17:26:26.147917Z",
     "iopub.status.busy": "2023-09-21T17:26:26.147159Z",
     "iopub.status.idle": "2023-09-21T17:27:11.130943Z",
     "shell.execute_reply": "2023-09-21T17:27:11.129875Z",
     "shell.execute_reply.started": "2023-09-21T17:26:26.147880Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Length GDB:  444285\n",
      "Trying FC(F)=C(F)C#CC#N\n",
      "Conformer:  F  -3.303279 -2.551231 -0.665592; C  -3.551114 -0.180504 -1.594233; F  -5.642254 0.510763 -2.775206; C  -1.480470 1.359424 -1.330889; F  -1.829597 3.736696 -2.292413; C  0.721395 0.525248 -0.394711; C  2.921869 -0.329714 0.586346; C  5.124244 -1.156335 1.526403; N 7.039206 -1.914347 2.335843; \n",
      "recompute: 33\n",
      ">>>  0 32\n",
      "_0_32\n",
      "0_GDB1_f32True_grid0_backendcpu_0_32\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "  0%|          | 0/33 [00:00<?, ?it/s]"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[PAD] Last molecule had grisize=9816 we're using 10797. \n",
      "[FC(F)(C#N)C(=O)C#N]\n",
      "[conformers] 32\n",
      "dft_iter: 16.4025 (45, 45, 45, 45) 15\n",
      "dft_iter: 7.77384 (4, 10797, 45) 20\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "[23 / 32] Hs=    0 -529.165139 1379.4 0.0 0.0 0.1 3.7 0.2 282.8 0.0 27.3 2.1 0.2 0.3 0.1 0.0 0.0 2.8 0.1 0.0 0.0 0.2 0.3 0.7 0.2 2.3 1702.8 [1 ; 0]:   0%|          | 0/33 [00:44<?, ?it/s]\n"
     ]
    },
    {
     "ename": "KeyboardInterrupt",
     "evalue": "",
     "output_type": "error",
     "traceback": [
      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
      "\u001b[0;31mKeyboardInterrupt\u001b[0m                         Traceback (most recent call last)",
      "\u001b[0;32m<ipython-input-8-ed004c1b245a>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m     28\u001b[0m     \u001b[0;32mbreak\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     29\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 30\u001b[0;31m \u001b[0mrecompute\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m0\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m0\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mour_fun\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mjax_dft\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mstr\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mstring\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
      "\u001b[0;32m/notebooks/pyscf_ipu/dft.py\u001b[0m in \u001b[0;36mrecompute\u001b[0;34m(args, molecules, id, num, our_fun, str, atom_string)\u001b[0m\n\u001b[1;32m   1142\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1143\u001b[0m   \u001b[0;32mif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0margs\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mskipus\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1144\u001b[0;31m     \u001b[0menergies\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mour_energy\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mour_hlgap\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mt_us\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mt_main_loop\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mus_hlgap\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mour_fun\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mstr\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0margs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   1145\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1146\u001b[0m   \u001b[0;32mif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0margs\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mskippyscf\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/notebooks/pyscf_ipu/dft.py\u001b[0m in \u001b[0;36mjax_dft\u001b[0;34m(str, args)\u001b[0m\n\u001b[1;32m   1327\u001b[0m     \u001b[0;32mfor\u001b[0m \u001b[0mstep\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mrange\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mrepeats\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1328\u001b[0m         \u001b[0mt0\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mtime\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtime\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1329\u001b[0;31m         \u001b[0mvals\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mdensity_functional_theory\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0matom_positions\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0margs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m   1330\u001b[0m         \u001b[0menergies\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0me_tot\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmo_energy\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmo_coeff\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdms\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mL_inv\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0mnp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0masarray\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0ma\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0ma\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mvals\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m   1331\u001b[0m         \u001b[0mt\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mtime\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtime\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m-\u001b[0m \u001b[0mt0\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;32m/notebooks/pyscf_ipu/dft.py\u001b[0m in \u001b[0;36mdensity_functional_theory\u001b[0;34m(atom_positions, args, mf_diis_space)\u001b[0m\n\u001b[1;32m    678\u001b[0m                 \u001b[0;32mif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0margs\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mforloop\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    679\u001b[0m                     \u001b[0;32mif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0margs\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mskip_minao\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mdensity_matrix\u001b[0m  \u001b[0;34m=\u001b[0m \u001b[0mnp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0marray\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mminao\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmol\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 680\u001b[0;31m                     \u001b[0mvals\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mappend\u001b[0m\u001b[0;34m(\u001b[0m \u001b[0mdo_compute_jit\u001b[0m\u001b[0;34m(\u001b[0m \u001b[0mdensity_matrix\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mkinetic\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mnuclear\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0moverlap\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mao\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0melectron_repulsion\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mweights\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mcoords\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mnuclear_energy\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m0\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmf_diis_space\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mN\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mhyb\u001b[0m \u001b[0;34m,\u001b[0m \u001b[0mmask\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0m_input_floats\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0m_input_ints\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdcargs\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mL_inv\u001b[0m\u001b[0;34m)\u001b[0m  \u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m    681\u001b[0m                 \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m    682\u001b[0m                     \u001b[0;31m# make this into a flag.\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
      "\u001b[0;31mKeyboardInterrupt\u001b[0m: "
     ]
    }
   ],
   "source": [
    "from rdkit import Chem\n",
    "\n",
    "from pyscf_ipu.dft import angstrom_to_bohr, get_atom_string, jax_dft, recompute\n",
    "\n",
    "print(\"Length GDB: \", len(args.smiles))\n",
    "\n",
    "if args.limit != -1:\n",
    "    args.smiles = args.smiles[:args.limit]\n",
    "\n",
    "for i in range(int(args.id), min(int(args.id)+1000, len(args.smiles))):\n",
    "    smile = args.smiles[i]\n",
    "\n",
    "    print('Trying', smile)\n",
    "\n",
    "    b = Chem.MolFromSmiles(smile)\n",
    "    b = Chem.AddHs(b, explicitOnly=False)\n",
    "\n",
    "    e = Chem.AllChem.EmbedMolecule(b)\n",
    "    if e == -1:\n",
    "       print('Did not embed', b) \n",
    "       continue\n",
    "\n",
    "    locs = b.GetConformer().GetPositions() * angstrom_to_bohr\n",
    "    atoms = [atom.GetSymbol() for atom in b.GetAtoms()]\n",
    "    atom_string, string = get_atom_string(\" \".join(atoms), locs)\n",
    "\n",
    "    print('Conformer: ', string)\n",
    "    break\n",
    "\n",
    "recompute(args, None, 0, 0, our_fun=jax_dft, str=string)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "e0ec0c9d",
   "metadata": {},
   "source": [
    "# Loading & visualizing generated data\n",
    "\n",
    "After the dataset has been created, we can load the data.\n",
    "(You may wish to spin up a new notebook, and view the data as \n",
    "it's being generated in this one)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "d778133f",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2023-09-21T17:27:59.930326Z",
     "iopub.status.busy": "2023-09-21T17:27:59.930089Z",
     "iopub.status.idle": "2023-09-21T17:27:59.934793Z",
     "shell.execute_reply": "2023-09-21T17:27:59.933812Z",
     "shell.execute_reply.started": "2023-09-21T17:27:59.930306Z"
    }
   },
   "outputs": [],
   "source": [
    "import pandas as pd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "3dfd2293",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2023-09-21T17:28:00.320279Z",
     "iopub.status.busy": "2023-09-21T17:28:00.319998Z",
     "iopub.status.idle": "2023-09-21T17:28:00.329206Z",
     "shell.execute_reply": "2023-09-21T17:28:00.328492Z",
     "shell.execute_reply.started": "2023-09-21T17:28:00.320258Z"
    }
   },
   "outputs": [],
   "source": [
    "# Output DFT dataset is a compressed CSV file.\n",
    "# NOTE: it may take a couple of minutes before the file is generated.\n",
    "rootpath = f'./data/generated/{args.fname}/'\n",
    "paths = sorted(os.listdir(rootpath), key=lambda x: os.path.getmtime(rootpath + x))\n",
    "filename = os.path.join(rootpath, paths[-1], \"data.csv\")\n",
    "\n",
    "df = pd.read_csv(filename, compression=\"gzip\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "b3e816e8",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2023-09-21T17:28:01.800043Z",
     "iopub.status.busy": "2023-09-21T17:28:01.799745Z",
     "iopub.status.idle": "2023-09-21T17:28:01.822706Z",
     "shell.execute_reply": "2023-09-21T17:28:01.821854Z",
     "shell.execute_reply.started": "2023-09-21T17:28:01.800021Z"
    }
   },
   "outputs": [
    {
     "data": {
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       "  <thead>\n",
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       "      <th></th>\n",
       "      <th>Unnamed: 0</th>\n",
       "      <th>smile</th>\n",
       "      <th>atoms</th>\n",
       "      <th>atom_positions</th>\n",
       "      <th>energies</th>\n",
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       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>0</td>\n",
       "      <td>FC(F)(C#N)C(=O)C#N</td>\n",
       "      <td>FCFCNCOCN</td>\n",
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       "      <td>[-14387.150902075824, -14321.477650378294, -14...</td>\n",
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       "      <td>-0.872470</td>\n",
       "      <td>4.999956</td>\n",
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       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>0</td>\n",
       "      <td>FC(F)(C#N)C(=O)C#N</td>\n",
       "      <td>FCFCNCOCN</td>\n",
       "      <td>[-2.3403320213763945, -1.054070549382328, 2.95...</td>\n",
       "      <td>[-14386.940987492488, -14327.730510746002, -14...</td>\n",
       "      <td>0.001410</td>\n",
       "      <td>[0.0]</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>[1.386e+03 8.000e-01 2.000e-01 2.000e-01 5.600...</td>\n",
       "      <td>-5.924247</td>\n",
       "      <td>-1.223614</td>\n",
       "      <td>4.700633</td>\n",
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       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>0</td>\n",
       "      <td>FC(F)(C#N)C(=O)C#N</td>\n",
       "      <td>FCFCNCOCN</td>\n",
       "      <td>[-2.508312250101616, -2.9848902777921023, 0.05...</td>\n",
       "      <td>[-14386.867679381283, -14319.960709000135, -14...</td>\n",
       "      <td>0.001749</td>\n",
       "      <td>[0.0]</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>[1.432e+03 1.000e-01 0.000e+00 1.000e-01 3.200...</td>\n",
       "      <td>-5.924836</td>\n",
       "      <td>-1.235037</td>\n",
       "      <td>4.689799</td>\n",
       "      <td>45</td>\n",
       "      <td>STO-3G</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>0</td>\n",
       "      <td>FC(F)(C#N)C(=O)C#N</td>\n",
       "      <td>FCFCNCOCN</td>\n",
       "      <td>[-3.2551803300125353, -2.1329334256170753, 0.8...</td>\n",
       "      <td>[-14387.076018358, -14329.75193126052, -14398....</td>\n",
       "      <td>0.001727</td>\n",
       "      <td>[0.0]</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>[1.4513e+03 0.0000e+00 0.0000e+00 1.0000e-01 3...</td>\n",
       "      <td>-5.899619</td>\n",
       "      <td>-1.169639</td>\n",
       "      <td>4.729980</td>\n",
       "      <td>45</td>\n",
       "      <td>STO-3G</td>\n",
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       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>0</td>\n",
       "      <td>FC(F)(C#N)C(=O)C#N</td>\n",
       "      <td>FCFCNCOCN</td>\n",
       "      <td>[-2.84609364909322, -2.7599543764642225, -0.10...</td>\n",
       "      <td>[-14386.926915515363, -14322.835535730032, -14...</td>\n",
       "      <td>0.001680</td>\n",
       "      <td>[0.0]</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>[1.3103e+03 0.0000e+00 0.0000e+00 1.0000e-01 2...</td>\n",
       "      <td>-5.838394</td>\n",
       "      <td>-1.148967</td>\n",
       "      <td>4.689428</td>\n",
       "      <td>45</td>\n",
       "      <td>STO-3G</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>0</td>\n",
       "      <td>FC(F)(C#N)C(=O)C#N</td>\n",
       "      <td>FCFCNCOCN</td>\n",
       "      <td>[-2.5512611780706536, -0.09244560716693372, 2....</td>\n",
       "      <td>[-14387.064401315674, -14325.209987703642, -14...</td>\n",
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       "      <td>0</td>\n",
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       "      <td>-5.920997</td>\n",
       "      <td>-1.230427</td>\n",
       "      <td>4.690571</td>\n",
       "      <td>45</td>\n",
       "      <td>STO-3G</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>0</td>\n",
       "      <td>FC(F)(C#N)C(=O)C#N</td>\n",
       "      <td>FCFCNCOCN</td>\n",
       "      <td>[-2.4575617356051964, -3.0864061240906833, -0....</td>\n",
       "      <td>[-14386.692958603096, -14324.748326944484, -14...</td>\n",
       "      <td>0.001462</td>\n",
       "      <td>[0.0]</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
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       "      <td>-5.964935</td>\n",
       "      <td>-1.271967</td>\n",
       "      <td>4.692968</td>\n",
       "      <td>45</td>\n",
       "      <td>STO-3G</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>0</td>\n",
       "      <td>FC(F)(C#N)C(=O)C#N</td>\n",
       "      <td>FCFCNCOCN</td>\n",
       "      <td>[-2.7357029092813003, -2.8385241218542117, -0....</td>\n",
       "      <td>[-14386.7613926158, -14324.300083556986, -1439...</td>\n",
       "      <td>0.001496</td>\n",
       "      <td>[0.0]</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>[1.295e+03 0.000e+00 0.000e+00 1.000e-01 2.900...</td>\n",
       "      <td>-5.921196</td>\n",
       "      <td>-1.042411</td>\n",
       "      <td>4.878785</td>\n",
       "      <td>45</td>\n",
       "      <td>STO-3G</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>0</td>\n",
       "      <td>FC(F)(C#N)C(=O)C#N</td>\n",
       "      <td>FCFCNCOCN</td>\n",
       "      <td>[-2.42430136622039, -0.706409910822915, -2.953...</td>\n",
       "      <td>[-14387.090781291115, -14328.945259046752, -14...</td>\n",
       "      <td>0.001376</td>\n",
       "      <td>[0.0]</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>[1.4328e+03 1.0000e-01 0.0000e+00 1.0000e-01 3...</td>\n",
       "      <td>-5.934455</td>\n",
       "      <td>-1.174914</td>\n",
       "      <td>4.759540</td>\n",
       "      <td>45</td>\n",
       "      <td>STO-3G</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>0</td>\n",
       "      <td>FC(F)(C#N)C(=O)C#N</td>\n",
       "      <td>FCFCNCOCN</td>\n",
       "      <td>[-3.1701050619634006, -2.335481199371203, 0.06...</td>\n",
       "      <td>[-14387.030638933082, -14324.197525311902, -14...</td>\n",
       "      <td>0.001235</td>\n",
       "      <td>[0.0]</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>[1.3675e+03 0.0000e+00 0.0000e+00 1.0000e-01 3...</td>\n",
       "      <td>-5.927952</td>\n",
       "      <td>-1.266243</td>\n",
       "      <td>4.661709</td>\n",
       "      <td>45</td>\n",
       "      <td>STO-3G</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>10</th>\n",
       "      <td>0</td>\n",
       "      <td>FC(F)(C#N)C(=O)C#N</td>\n",
       "      <td>FCFCNCOCN</td>\n",
       "      <td>[-0.4955235145604512, -3.815391262169907, 1.06...</td>\n",
       "      <td>[-14387.03486542885, -14321.65699116902, -1439...</td>\n",
       "      <td>0.001234</td>\n",
       "      <td>[0.0]</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>[1.3478e+03 0.0000e+00 0.0000e+00 1.0000e-01 2...</td>\n",
       "      <td>-5.902995</td>\n",
       "      <td>-1.239800</td>\n",
       "      <td>4.663195</td>\n",
       "      <td>45</td>\n",
       "      <td>STO-3G</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>11</th>\n",
       "      <td>0</td>\n",
       "      <td>FC(F)(C#N)C(=O)C#N</td>\n",
       "      <td>FCFCNCOCN</td>\n",
       "      <td>[-2.896145568625801, -2.6944503417478223, 0.04...</td>\n",
       "      <td>[-14387.180671110935, -14329.323375554111, -14...</td>\n",
       "      <td>0.000544</td>\n",
       "      <td>[0.0]</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>[1.4026e+03 3.0000e-01 2.0000e-01 2.0000e-01 5...</td>\n",
       "      <td>-5.917533</td>\n",
       "      <td>-1.078833</td>\n",
       "      <td>4.838700</td>\n",
       "      <td>45</td>\n",
       "      <td>STO-3G</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>12</th>\n",
       "      <td>0</td>\n",
       "      <td>FC(F)(C#N)C(=O)C#N</td>\n",
       "      <td>FCFCNCOCN</td>\n",
       "      <td>[-3.448789435155949, -1.9135614246323718, -0.2...</td>\n",
       "      <td>[-14386.95869711719, -14324.17509990307, -1439...</td>\n",
       "      <td>0.000551</td>\n",
       "      <td>[0.0]</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>[1.3035e+03 1.0000e-01 0.0000e+00 1.0000e-01 2...</td>\n",
       "      <td>-5.903519</td>\n",
       "      <td>-1.232730</td>\n",
       "      <td>4.670790</td>\n",
       "      <td>45</td>\n",
       "      <td>STO-3G</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>13</th>\n",
       "      <td>0</td>\n",
       "      <td>FC(F)(C#N)C(=O)C#N</td>\n",
       "      <td>FCFCNCOCN</td>\n",
       "      <td>[-0.8669695806667599, -3.388088649845672, 1.85...</td>\n",
       "      <td>[-14386.79277249616, -14327.145576278795, -143...</td>\n",
       "      <td>0.001521</td>\n",
       "      <td>[0.0]</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>[1.3845e+03 2.0000e-01 1.0000e-01 3.0000e-01 6...</td>\n",
       "      <td>-5.854690</td>\n",
       "      <td>-1.131749</td>\n",
       "      <td>4.722942</td>\n",
       "      <td>45</td>\n",
       "      <td>STO-3G</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>14</th>\n",
       "      <td>0</td>\n",
       "      <td>FC(F)(C#N)C(=O)C#N</td>\n",
       "      <td>FCFCNCOCN</td>\n",
       "      <td>[-1.8848237401881731, -2.1472662490216803, 1.6...</td>\n",
       "      <td>[-14387.739973912656, -14336.080636989258, -14...</td>\n",
       "      <td>0.001136</td>\n",
       "      <td>[0.0]</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>[1.3781e+03 0.0000e+00 0.0000e+00 1.0000e-01 3...</td>\n",
       "      <td>-5.815578</td>\n",
       "      <td>-1.267300</td>\n",
       "      <td>4.548279</td>\n",
       "      <td>45</td>\n",
       "      <td>STO-3G</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>15</th>\n",
       "      <td>0</td>\n",
       "      <td>FC(F)(C#N)C(=O)C#N</td>\n",
       "      <td>FCFCNCOCN</td>\n",
       "      <td>[0.7052799833000835, -2.246904661007722, -3.05...</td>\n",
       "      <td>[-14384.332974702002, -14300.881901333787, -14...</td>\n",
       "      <td>0.001447</td>\n",
       "      <td>[0.0]</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>[1.2682e+03 0.0000e+00 0.0000e+00 1.0000e-01 2...</td>\n",
       "      <td>-5.435834</td>\n",
       "      <td>0.013034</td>\n",
       "      <td>5.448868</td>\n",
       "      <td>45</td>\n",
       "      <td>STO-3G</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>16</th>\n",
       "      <td>0</td>\n",
       "      <td>FC(F)(C#N)C(=O)C#N</td>\n",
       "      <td>FCFCNCOCN</td>\n",
       "      <td>[-2.171671209126482, -2.888501784031278, -1.60...</td>\n",
       "      <td>[-14387.113524688302, -14326.735076174467, -14...</td>\n",
       "      <td>0.001817</td>\n",
       "      <td>[0.0]</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>[1.4629e+03 0.0000e+00 0.0000e+00 1.0000e-01 2...</td>\n",
       "      <td>-5.841239</td>\n",
       "      <td>-1.084818</td>\n",
       "      <td>4.756420</td>\n",
       "      <td>45</td>\n",
       "      <td>STO-3G</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17</th>\n",
       "      <td>0</td>\n",
       "      <td>FC(F)(C#N)C(=O)C#N</td>\n",
       "      <td>FCFCNCOCN</td>\n",
       "      <td>[-1.710188439380679, -2.702621686452995, 2.293...</td>\n",
       "      <td>[-14387.13593990543, -14326.763387395, -14398....</td>\n",
       "      <td>0.002308</td>\n",
       "      <td>[0.0]</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>[1.4376e+03 0.0000e+00 0.0000e+00 1.0000e-01 3...</td>\n",
       "      <td>-5.880317</td>\n",
       "      <td>-1.198676</td>\n",
       "      <td>4.681641</td>\n",
       "      <td>45</td>\n",
       "      <td>STO-3G</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>18</th>\n",
       "      <td>0</td>\n",
       "      <td>FC(F)(C#N)C(=O)C#N</td>\n",
       "      <td>FCFCNCOCN</td>\n",
       "      <td>[-3.4057943826886565, -1.561154489323613, 1.28...</td>\n",
       "      <td>[-14386.9272498957, -14326.420290319717, -1439...</td>\n",
       "      <td>0.001696</td>\n",
       "      <td>[0.0]</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>[1.3925e+03 0.0000e+00 0.0000e+00 1.0000e-01 2...</td>\n",
       "      <td>-5.849538</td>\n",
       "      <td>-1.185962</td>\n",
       "      <td>4.663575</td>\n",
       "      <td>45</td>\n",
       "      <td>STO-3G</td>\n",
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       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>0</td>\n",
       "      <td>FC(F)(C#N)C(=O)C#N</td>\n",
       "      <td>FCFCNCOCN</td>\n",
       "      <td>[-1.9708144435369819, -3.327291089234618, -0.0...</td>\n",
       "      <td>[-14386.895978053113, -14324.132897142825, -14...</td>\n",
       "      <td>0.000951</td>\n",
       "      <td>[0.0]</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>[1.385e+03 1.000e-01 0.000e+00 1.000e-01 3.200...</td>\n",
       "      <td>-5.976503</td>\n",
       "      <td>-1.212600</td>\n",
       "      <td>4.763903</td>\n",
       "      <td>45</td>\n",
       "      <td>STO-3G</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>20</th>\n",
       "      <td>0</td>\n",
       "      <td>FC(F)(C#N)C(=O)C#N</td>\n",
       "      <td>FCFCNCOCN</td>\n",
       "      <td>[-3.0388700018391934, -1.424549775933863, 2.16...</td>\n",
       "      <td>[-14387.046482045282, -14323.971142266193, -14...</td>\n",
       "      <td>0.001052</td>\n",
       "      <td>[0.0]</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>[1.3807e+03 1.0000e-01 0.0000e+00 1.0000e-01 2...</td>\n",
       "      <td>-5.880249</td>\n",
       "      <td>-1.114917</td>\n",
       "      <td>4.765332</td>\n",
       "      <td>45</td>\n",
       "      <td>STO-3G</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21</th>\n",
       "      <td>0</td>\n",
       "      <td>FC(F)(C#N)C(=O)C#N</td>\n",
       "      <td>FCFCNCOCN</td>\n",
       "      <td>[-0.22353180805978884, -3.849116405960359, -0....</td>\n",
       "      <td>[-14386.735734917036, -14325.886920164316, -14...</td>\n",
       "      <td>0.001624</td>\n",
       "      <td>[0.0]</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>[1.3943e+03 0.0000e+00 0.0000e+00 1.0000e-01 2...</td>\n",
       "      <td>-6.052645</td>\n",
       "      <td>-1.246926</td>\n",
       "      <td>4.805719</td>\n",
       "      <td>45</td>\n",
       "      <td>STO-3G</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>0</td>\n",
       "      <td>FC(F)(C#N)C(=O)C#N</td>\n",
       "      <td>FCFCNCOCN</td>\n",
       "      <td>[-2.453279357441664, -2.704595223076375, 0.606...</td>\n",
       "      <td>[-14386.986872654463, -14324.686839346645, -14...</td>\n",
       "      <td>0.000837</td>\n",
       "      <td>[0.0]</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>[1.3794e+03 0.0000e+00 0.0000e+00 1.0000e-01 3...</td>\n",
       "      <td>-5.866542</td>\n",
       "      <td>-1.127568</td>\n",
       "      <td>4.738974</td>\n",
       "      <td>45</td>\n",
       "      <td>STO-3G</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "    Unnamed: 0               smile      atoms  \\\n",
       "0            0  FC(F)(C#N)C(=O)C#N  FCFCNCOCN   \n",
       "1            0  FC(F)(C#N)C(=O)C#N  FCFCNCOCN   \n",
       "2            0  FC(F)(C#N)C(=O)C#N  FCFCNCOCN   \n",
       "3            0  FC(F)(C#N)C(=O)C#N  FCFCNCOCN   \n",
       "4            0  FC(F)(C#N)C(=O)C#N  FCFCNCOCN   \n",
       "5            0  FC(F)(C#N)C(=O)C#N  FCFCNCOCN   \n",
       "6            0  FC(F)(C#N)C(=O)C#N  FCFCNCOCN   \n",
       "7            0  FC(F)(C#N)C(=O)C#N  FCFCNCOCN   \n",
       "8            0  FC(F)(C#N)C(=O)C#N  FCFCNCOCN   \n",
       "9            0  FC(F)(C#N)C(=O)C#N  FCFCNCOCN   \n",
       "10           0  FC(F)(C#N)C(=O)C#N  FCFCNCOCN   \n",
       "11           0  FC(F)(C#N)C(=O)C#N  FCFCNCOCN   \n",
       "12           0  FC(F)(C#N)C(=O)C#N  FCFCNCOCN   \n",
       "13           0  FC(F)(C#N)C(=O)C#N  FCFCNCOCN   \n",
       "14           0  FC(F)(C#N)C(=O)C#N  FCFCNCOCN   \n",
       "15           0  FC(F)(C#N)C(=O)C#N  FCFCNCOCN   \n",
       "16           0  FC(F)(C#N)C(=O)C#N  FCFCNCOCN   \n",
       "17           0  FC(F)(C#N)C(=O)C#N  FCFCNCOCN   \n",
       "18           0  FC(F)(C#N)C(=O)C#N  FCFCNCOCN   \n",
       "19           0  FC(F)(C#N)C(=O)C#N  FCFCNCOCN   \n",
       "20           0  FC(F)(C#N)C(=O)C#N  FCFCNCOCN   \n",
       "21           0  FC(F)(C#N)C(=O)C#N  FCFCNCOCN   \n",
       "22           0  FC(F)(C#N)C(=O)C#N  FCFCNCOCN   \n",
       "\n",
       "                                       atom_positions  \\\n",
       "0   [0.15332033500393688, -2.3606980417798886, -2....   \n",
       "1   [-2.3403320213763945, -1.054070549382328, 2.95...   \n",
       "2   [-2.508312250101616, -2.9848902777921023, 0.05...   \n",
       "3   [-3.2551803300125353, -2.1329334256170753, 0.8...   \n",
       "4   [-2.84609364909322, -2.7599543764642225, -0.10...   \n",
       "5   [-2.5512611780706536, -0.09244560716693372, 2....   \n",
       "6   [-2.4575617356051964, -3.0864061240906833, -0....   \n",
       "7   [-2.7357029092813003, -2.8385241218542117, -0....   \n",
       "8   [-2.42430136622039, -0.706409910822915, -2.953...   \n",
       "9   [-3.1701050619634006, -2.335481199371203, 0.06...   \n",
       "10  [-0.4955235145604512, -3.815391262169907, 1.06...   \n",
       "11  [-2.896145568625801, -2.6944503417478223, 0.04...   \n",
       "12  [-3.448789435155949, -1.9135614246323718, -0.2...   \n",
       "13  [-0.8669695806667599, -3.388088649845672, 1.85...   \n",
       "14  [-1.8848237401881731, -2.1472662490216803, 1.6...   \n",
       "15  [0.7052799833000835, -2.246904661007722, -3.05...   \n",
       "16  [-2.171671209126482, -2.888501784031278, -1.60...   \n",
       "17  [-1.710188439380679, -2.702621686452995, 2.293...   \n",
       "18  [-3.4057943826886565, -1.561154489323613, 1.28...   \n",
       "19  [-1.9708144435369819, -3.327291089234618, -0.0...   \n",
       "20  [-3.0388700018391934, -1.424549775933863, 2.16...   \n",
       "21  [-0.22353180805978884, -3.849116405960359, -0....   \n",
       "22  [-2.453279357441664, -2.704595223076375, 0.606...   \n",
       "\n",
       "                                             energies       std  \\\n",
       "0   [-14387.150902075824, -14321.477650378294, -14...  0.000685   \n",
       "1   [-14386.940987492488, -14327.730510746002, -14...  0.001410   \n",
       "2   [-14386.867679381283, -14319.960709000135, -14...  0.001749   \n",
       "3   [-14387.076018358, -14329.75193126052, -14398....  0.001727   \n",
       "4   [-14386.926915515363, -14322.835535730032, -14...  0.001680   \n",
       "5   [-14387.064401315674, -14325.209987703642, -14...  0.001245   \n",
       "6   [-14386.692958603096, -14324.748326944484, -14...  0.001462   \n",
       "7   [-14386.7613926158, -14324.300083556986, -1439...  0.001496   \n",
       "8   [-14387.090781291115, -14328.945259046752, -14...  0.001376   \n",
       "9   [-14387.030638933082, -14324.197525311902, -14...  0.001235   \n",
       "10  [-14387.03486542885, -14321.65699116902, -1439...  0.001234   \n",
       "11  [-14387.180671110935, -14329.323375554111, -14...  0.000544   \n",
       "12  [-14386.95869711719, -14324.17509990307, -1439...  0.000551   \n",
       "13  [-14386.79277249616, -14327.145576278795, -143...  0.001521   \n",
       "14  [-14387.739973912656, -14336.080636989258, -14...  0.001136   \n",
       "15  [-14384.332974702002, -14300.881901333787, -14...  0.001447   \n",
       "16  [-14387.113524688302, -14326.735076174467, -14...  0.001817   \n",
       "17  [-14387.13593990543, -14326.763387395, -14398....  0.002308   \n",
       "18  [-14386.9272498957, -14326.420290319717, -1439...  0.001696   \n",
       "19  [-14386.895978053113, -14324.132897142825, -14...  0.000951   \n",
       "20  [-14387.046482045282, -14323.971142266193, -14...  0.001052   \n",
       "21  [-14386.735734917036, -14325.886920164316, -14...  0.001624   \n",
       "22  [-14386.986872654463, -14324.686839346645, -14...  0.000837   \n",
       "\n",
       "   pyscf_energies  pyscf_hlgap  pyscf_homo  pyscf_lumo  \\\n",
       "0           [0.0]            0           0           0   \n",
       "1           [0.0]            0           0           0   \n",
       "2           [0.0]            0           0           0   \n",
       "3           [0.0]            0           0           0   \n",
       "4           [0.0]            0           0           0   \n",
       "5           [0.0]            0           0           0   \n",
       "6           [0.0]            0           0           0   \n",
       "7           [0.0]            0           0           0   \n",
       "8           [0.0]            0           0           0   \n",
       "9           [0.0]            0           0           0   \n",
       "10          [0.0]            0           0           0   \n",
       "11          [0.0]            0           0           0   \n",
       "12          [0.0]            0           0           0   \n",
       "13          [0.0]            0           0           0   \n",
       "14          [0.0]            0           0           0   \n",
       "15          [0.0]            0           0           0   \n",
       "16          [0.0]            0           0           0   \n",
       "17          [0.0]            0           0           0   \n",
       "18          [0.0]            0           0           0   \n",
       "19          [0.0]            0           0           0   \n",
       "20          [0.0]            0           0           0   \n",
       "21          [0.0]            0           0           0   \n",
       "22          [0.0]            0           0           0   \n",
       "\n",
       "                                                times      homo      lumo  \\\n",
       "0   [4.5475e+03 0.0000e+00 0.0000e+00 1.0000e-01 3... -5.872426 -0.872470   \n",
       "1   [1.386e+03 8.000e-01 2.000e-01 2.000e-01 5.600... -5.924247 -1.223614   \n",
       "2   [1.432e+03 1.000e-01 0.000e+00 1.000e-01 3.200... -5.924836 -1.235037   \n",
       "3   [1.4513e+03 0.0000e+00 0.0000e+00 1.0000e-01 3... -5.899619 -1.169639   \n",
       "4   [1.3103e+03 0.0000e+00 0.0000e+00 1.0000e-01 2... -5.838394 -1.148967   \n",
       "5   [1.3518e+03 1.0000e-01 0.0000e+00 1.0000e-01 3... -5.920997 -1.230427   \n",
       "6   [1.3116e+03 1.0000e-01 0.0000e+00 1.0000e-01 2... -5.964935 -1.271967   \n",
       "7   [1.295e+03 0.000e+00 0.000e+00 1.000e-01 2.900... -5.921196 -1.042411   \n",
       "8   [1.4328e+03 1.0000e-01 0.0000e+00 1.0000e-01 3... -5.934455 -1.174914   \n",
       "9   [1.3675e+03 0.0000e+00 0.0000e+00 1.0000e-01 3... -5.927952 -1.266243   \n",
       "10  [1.3478e+03 0.0000e+00 0.0000e+00 1.0000e-01 2... -5.902995 -1.239800   \n",
       "11  [1.4026e+03 3.0000e-01 2.0000e-01 2.0000e-01 5... -5.917533 -1.078833   \n",
       "12  [1.3035e+03 1.0000e-01 0.0000e+00 1.0000e-01 2... -5.903519 -1.232730   \n",
       "13  [1.3845e+03 2.0000e-01 1.0000e-01 3.0000e-01 6... -5.854690 -1.131749   \n",
       "14  [1.3781e+03 0.0000e+00 0.0000e+00 1.0000e-01 3... -5.815578 -1.267300   \n",
       "15  [1.2682e+03 0.0000e+00 0.0000e+00 1.0000e-01 2... -5.435834  0.013034   \n",
       "16  [1.4629e+03 0.0000e+00 0.0000e+00 1.0000e-01 2... -5.841239 -1.084818   \n",
       "17  [1.4376e+03 0.0000e+00 0.0000e+00 1.0000e-01 3... -5.880317 -1.198676   \n",
       "18  [1.3925e+03 0.0000e+00 0.0000e+00 1.0000e-01 2... -5.849538 -1.185962   \n",
       "19  [1.385e+03 1.000e-01 0.000e+00 1.000e-01 3.200... -5.976503 -1.212600   \n",
       "20  [1.3807e+03 1.0000e-01 0.0000e+00 1.0000e-01 2... -5.880249 -1.114917   \n",
       "21  [1.3943e+03 0.0000e+00 0.0000e+00 1.0000e-01 2... -6.052645 -1.246926   \n",
       "22  [1.3794e+03 0.0000e+00 0.0000e+00 1.0000e-01 3... -5.866542 -1.127568   \n",
       "\n",
       "       hlgap   N   basis  \n",
       "0   4.999956  45  STO-3G  \n",
       "1   4.700633  45  STO-3G  \n",
       "2   4.689799  45  STO-3G  \n",
       "3   4.729980  45  STO-3G  \n",
       "4   4.689428  45  STO-3G  \n",
       "5   4.690571  45  STO-3G  \n",
       "6   4.692968  45  STO-3G  \n",
       "7   4.878785  45  STO-3G  \n",
       "8   4.759540  45  STO-3G  \n",
       "9   4.661709  45  STO-3G  \n",
       "10  4.663195  45  STO-3G  \n",
       "11  4.838700  45  STO-3G  \n",
       "12  4.670790  45  STO-3G  \n",
       "13  4.722942  45  STO-3G  \n",
       "14  4.548279  45  STO-3G  \n",
       "15  5.448868  45  STO-3G  \n",
       "16  4.756420  45  STO-3G  \n",
       "17  4.681641  45  STO-3G  \n",
       "18  4.663575  45  STO-3G  \n",
       "19  4.763903  45  STO-3G  \n",
       "20  4.765332  45  STO-3G  \n",
       "21  4.805719  45  STO-3G  \n",
       "22  4.738974  45  STO-3G  "
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "9cd76867",
   "metadata": {
    "execution": {
     "iopub.execute_input": "2023-09-21T17:28:08.148775Z",
     "iopub.status.busy": "2023-09-21T17:28:08.148512Z",
     "iopub.status.idle": "2023-09-21T17:28:08.154608Z",
     "shell.execute_reply": "2023-09-21T17:28:08.153901Z",
     "shell.execute_reply.started": "2023-09-21T17:28:08.148754Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0     4.999956\n",
       "1     4.700633\n",
       "2     4.689799\n",
       "3     4.729980\n",
       "4     4.689428\n",
       "5     4.690571\n",
       "6     4.692968\n",
       "7     4.878785\n",
       "8     4.759540\n",
       "9     4.661709\n",
       "10    4.663195\n",
       "11    4.838700\n",
       "12    4.670790\n",
       "13    4.722942\n",
       "14    4.548279\n",
       "15    5.448868\n",
       "16    4.756420\n",
       "17    4.681641\n",
       "18    4.663575\n",
       "19    4.763903\n",
       "20    4.765332\n",
       "21    4.805719\n",
       "22    4.738974\n",
       "Name: hlgap, dtype: float64"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# HLgap data.\n",
    "df[\"hlgap\"]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "fb46e364-e56f-48b5-8be5-c913444e9c07",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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